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// $Id: SubstructUtils.cpp 1625 2011-01-13 04:22:56Z glandrum $
//
// Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "SubstructUtils.h"
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <boost/dynamic_bitset.hpp>
namespace RDKit{
bool atomCompat(const ATOM_SPTR a1,const ATOM_SPTR a2){
PRECONDITION(a1,"bad atom");
PRECONDITION(a2,"bad atom");
//std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 << " " << a2->getIdx() << std::endl;
bool res = a1->Match(a2);
return res;
}
bool chiralAtomCompat(const ATOM_SPTR a1,const ATOM_SPTR a2){
PRECONDITION(a1,"bad atom");
PRECONDITION(a2,"bad atom");
//std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 << " " << a2->getIdx() << std::endl;
bool res = a1->Match(a2);
if(res){
if(a1->hasProp("_CIPCode") || a2->hasProp("_CIPCode")){
// if either atom has a CIPCode, they need to both have it and match:
if(a1->hasProp("_CIPCode") && a2->hasProp("_CIPCode")){
std::string s1,s2;
a1->getProp("_CIPCode",s1);
a2->getProp("_CIPCode",s2);
if(s1!=s2) res=false;
} else {
res=false;
}
}
}
return res;
}
bool bondCompat(const BOND_SPTR b1,const BOND_SPTR b2){
PRECONDITION(b1,"bad bond");
PRECONDITION(b2,"bad bond");
bool res = b1->Match(b2);
//std::cout << "\t\tbondCompat: "<< b1->getIdx() << "-" << b2->getIdx() << ": " << res << std::endl;
return res;
}
void removeDuplicates(std::vector<MatchVectType> &v,unsigned int nAtoms){
//
// This works by tracking the indices of the atoms in each match vector.
// This can lead to unexpected behavior when looking at rings and queries
// that don't specify bond orders. For example querying this molecule:
// C1CCC=1
// with the pattern constructed from SMARTS C~C~C~C will return a
// single match, despite the fact that there are 4 different paths
// when valence is considered. The defense of this behavior is
// that the 4 paths are equivalent in the semantics of the query.
// Also, OELib returns the same results
//
std::vector< boost::dynamic_bitset<> > seen;
std::vector<MatchVectType> res;
for(std::vector<MatchVectType>::const_iterator i=v.begin();i!=v.end();++i){
boost::dynamic_bitset<> val(nAtoms);
for(MatchVectType::const_iterator ci=i->begin();ci!=i->end();++ci){
val.set(ci->second);
}
if(std::find(seen.begin(),seen.end(),val)==seen.end()){
// it's something new
res.push_back(*i);
seen.push_back(val);
}
}
v = res;
}
}
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